☰ Navigation Tabs
Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with NF2376
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EEM PDB entry 5EEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 10 mg/mL HDAC6 CD2 Protein,
2 mM NF2376 Inhibitor,
0.2 M Ammonium Phosphate Dibasic,
20% peg 3350,
1:1 ratio protein to precipitant
Crystal Properties Matthews coefficient Solvent content 2.41 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.252 α = 90 b = 108.135 β = 90.013 c = 74.345 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.039 74.4 96.2 0.174 0.112 0.982 5.6 3.4 46684 22.1643747285
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.11 95.8 0.767 0.498 0.662 1.3 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 5EEM 2.03951514036 74.3449980863 1.36375430773 46684 2279 96.1050724638 0.196922853602 0.194959732075 0.1959 0.234196557526 0.2355 24.0467582879
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.3647356349 f_angle_d 0.926080663182 f_chiral_restr 0.0534327920353 f_bond_d 0.00748267369847 f_plane_restr 0.00592743336893
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5477 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 66
Software Software Software Name Purpose PHENIX refinement iMOSFLM data reduction Aimless data scaling PHASER phasing